To achieve acute and sensitive vision in a camera-like eye in the ocean, a graded refractive index spherical lens is required to maximize the photon flux on the retina, while leaving an eye structure that fits in the head of an animal. This biological lens must also maintain low protein density fluctuation at the length-scale of a wavelength of visible light in order to maintain transparency. In squids, this sophisticated optical design emerges from the properties of a single protein fold, the S-crystallin. In this thesis, I study the material properties and the self-assembly of the squid lens system. I show that squids have evolved graded index and low density fluctuation in a spherical lens using a suite of proteins that can act as patchy colloids with specific, low valence (M=2 or M=3) with geometric flexibility in bond angles. We conducted small x-ray scattering (SAXS) at different radial positions of the lens, and performed a Monte Carlo simulation to estimate structures consistent with the SAXS result. This analysis suggests that lens proteins may form a gel with gradient density throughout the cellular lens structure, with density mediated by a tightly controlled protein coordination number in each region of the organ. Patchy colloid theory may therefore explain both the graded refractive index lens and the transparency evolved in the lens. I also studied the Chinese century egg, which appears to be a physically analogous system of a protein-based, low-valence patchy colloidal gel that was developed in prehistoric Chinese culinary culture as a method of egg preservation. I compare the structure and material properties of these two systems.